BZP, a novel serum-responsive zinc finger protein that inhibits gene transcription

Evolutionary functional analysis and molecular regulation of the ZEB transcription factors

ZEB1 and ZEB2, which are members of the ZEB family of transcription factors, play a pivotal role in the development of the vertebrate embryo. However, recent evidence shows that both proteins can also drive the process of epithelial-mesenchymal transition during malignant cancer progression. The understanding of how both ZEBs act as transcription factors opens up new possibilities for future treatment of advanced carcinomas. This review gives insight into the molecular mechanisms that form the basis of the multitude of cellular processes controlled by both ZEB factors. By using an evolutionary approach, we analyzed how the specific organization of the different domains and regulatory sites in ZEB1 and ZEB2 came into existence. On the basis of this analysis, a detailed overview is provided of the different cofactors and post-translational mechanisms that are associated with ZEB protein functionality.

Expanding roles of ZEB factors in tumorigenesis and tumor progression

The ZEB family of transcription factors regulates key factors during embryonic development and cell differentiation but their role in cancer biology has only more recently begun to be recognized. Early evidence showed that ZEB proteins induce an epithelial-to-mesenchymal transition linking their expression with increased aggressiveness and metastasis in mice models and a wide range of primary human carcinomas. Reports over the last few years have found that ZEB proteins also play critical roles in the maintenance of cancer cell stemness, control of replicative senescence, tumor angiogenesis, overcoming of oncogenic addiction and resistance to chemotherapy. These expanding roles in tumorigenesis and tumor progression set ZEB proteins as potential diagnostic, prognostic and therapeutic targets.

delta-EF1 is a negative regulator of Ihh in the developing growth plate

Indian hedgehog (Ihh) regulates proliferation and differentiation of chondrocytes in the growth plate. Although the biology of Ihh is currently well documented, its transcriptional regulation is poorly understood. delta-EF1 is a two-handed zinc finger/homeodomain transcriptional repressor. Targeted inactivation of mouse delta-EF1 leads to skeletal abnormalities including disorganized growth plates, shortening of long bones, and joint fusions, which are reminiscent of defects associated with deregulation of Ihh signaling. Here, we show that the absence of delta-EF1 results in delayed hypertrophic differentiation of chondrocytes and increased cell proliferation in the growth plate. Further, we demonstrate that delta-EF1 binds to the putative regulatory elements in intron 1 of Ihh in vitro and in vivo, resulting in down-regulation of Ihh expression. Finally, we show that delta-EF1 haploinsufficiency leads to a postnatal increase in trabecular bone mass associated with enhanced Ihh expression. In summary, we have identified delta-EF1 as an in vivo negative regulator of Ihh expression in the growth plate.

BMP-6 promotes E-cadherin expression through repressing deltaEF1 in breast cancer cells

BACKGROUND

Bone morphogenetic protein-6 (BMP-6) is critically involved in many developmental processes. Recent studies indicate that BMP-6 is closely related to tumor differentiation and metastasis.

METHODS

Quantitative RT-PCR was used to determine the expression of BMP-6, E-cadherin, and deltaEF1 at the mRNA level in MCF-7 and MDA-MB-231 breast cancer cells, as well as in 16 breast cancer specimens. Immunoblot analysis was used to measure the expression of deltaEF1 at the protein level in deltaEF1-overexpressing and deltaEF1-interfered MDA-MB-231 cells. Luciferase assay was used to determine the rhBMP-6 or deltaEF1 driven transcriptional activity of the E-cadherin promoter in MDA-MB-231 cells. Quantitative CHIP assay was used to detect the direct association of deltaEF1 with the E-cadherin proximal promoter in MDA-MB-231 cells.

RESULTS

MCF-7 breast cancer cells, an ER+ cell line that expressed high levels of BMP-6 and E-cadherin exhibited very low levels of deltaEF1 transcript. In contrast, MDA-MB-231 cells, an ER- cell line had significantly reduced BMP-6 and E-cadherin mRNA levels, suggesting an inverse correlation between BMP-6/E-cadherin and deltaEF1. To determine if the same relationship exists in human tumors, we examined tissue samples of breast cancer from human subjects. In 16 breast cancer specimens, the inverse correlation between BMP-6/E-cadherin and deltaEF1 was observed in both ER+ cases (4 of 8 cases) and ER- cases (7 of 8 cases). Further, we found that BMP-6 inhibited deltaEF1 transcription, resulting in an up-regulation of E-cadherin mRNA expression. This is consistent with our analysis of the E-cadherin promoter demonstrating that BMP-6 was a potent transcriptional activator. Interestingly, ectopic expression of deltaEF1 was able to block BMP-6-induced transactivation of E-cadherin, whereas RNA interference-mediated down-regulation of endogenous deltaEF1 in breast cancer cells abolished E-cadherin transactivation by BMP-6. In addition to down-regulating the expression of deltaEF1, BMP-6 also physically dislodged deltaEF1 from E-cadherin promoter to allow the activation of E-cadherin transcription.

CONCLUSION

We conclude that repression of deltaEF1 plays a key role in mediating BMP-6-induced transcriptional activation of E-cadherin in breast cancer cells. Consistent with the fact that higher level of deltaEF1 expression is associated with more invasive phenotype of breast cancer cells, our collective data suggests that deltaEF1 is likely the switch through which BMP-6 restores E-cadherin-mediated cell-to-cell adhesion and prevents breast cancer metastasis.

deltaEF1 represses BMP-2-induced differentiation of C2C12 myoblasts into the osteoblast lineage

Osteoblasts, derived from pluripotent mesenchymal precursor cells, acquire their differentiated phenotypes under the control of a series of regulatory factors, the best known of which is BMP-2. Our recent preliminary studies suggest that expression of deltaEF1, a member of the zinc finger-homeodomain transcription factor family, is significantly down-regulated as human mesenchymal stem cells (MSCs) are subjected to osteoblastic differentiation in the presence of BMP-2. Here we demonstrate that overexpression of deltaEF1 in murine pre-myoblast C2C12 cells resulted in a decrease in the mRNA levels of early osteoblast marker genes induced by BMP-2 including osterix and collagen type I. This inhibitory effect was further confirmed by decreased alkaline phosphatase (ALP) activities. Neither of the zinc finger clusters of deltaEF1 is necessary for its repressive effect on BMP-2-induced osteoblastic differentiation of C2C12 cells. Immunoprecipitation results indicated that deltaEF1 did not physically associate with Smads proteins, suggesting that the inhibitory effect of deltaEF1 may be Smad-independent. deltaEF1 overexpression in C2C12 cells resulted in down-regulation of activating protein-1 (AP-1) activities promoted by BMP-2. Moreover, deltaEF1 exhibited transrepression on murine osteocalcin gene which effect is partially mediated through diminishing of AP-1 signaling. These results suggest that deltaEF1 acts as a potent inhibitor of BMP-2-induced osteogenesis in vitro, in part, by differentially regulating the AP-1 signaling pathway.

A locus for posterior polymorphous corneal dystrophy (PPCD3) maps to chromosome 10

Posterior polymorphous corneal dystrophy (PPCD) is an autosomal dominant disorder characterized by corneal endothelial abnormalities, which can lead to blindness due to loss of corneal transparency and sometimes glaucoma. We mapped a new locus responsible for PPCD in a family in which we excluded the previously reported PPCD locus on 20q11, and the region containing COL8A2 on chromosome 1. Results of a 317-marker genome scan provided significant evidence of linkage of PPCD to markers on chromosome 10, with single-point LOD scores of 2.63, 1.63, and 3.19 for markers D10S208 (at (circumflex)theta = 0.03), D10S1780 (at (circumflex)theta = 0.00), and D10S578 (at (circumflex)theta = 0.06). A maximum multi-point LOD score of 4.35 was found at marker D10S1780. Affected family members shared a haplotype in an 8.55 cM critical interval that was bounded by markers D10S213 and D10S578. Our finding of another PPCD locus, PPCD3, on chromosome 10 indicates that PPCD is genetically heterogeneous. Guttae, a common corneal finding sometimes observed along with PPCD, were found among both affected and unaffected members of the proband's sib ship, but were absent in the younger generations of the family. Evaluation of phenotypic differences between family members sharing the same affected haplotype raises questions about whether differences in disease severity, including differences in response to surgical interventions, could be due to genetic background or other factors independent of the PPCD3 locus.

Rainbow tags: a visual tag system for recombinant protein expression and purification

Visualization systems for tracking proteins are standard experimental tools in most areas of biological research apart from protein purification. Here, we have sought to plug this gap by producing red and yellow visual tags using the heme-binding domain of mosquito cytochrome b5 and the flavin mononucleotide (FMN)-binding domain of human P450 reductase. Tests with colorless glutathione-S-transferase (GST) show them to be simple and effective tools for visually identifying correctly folded protein and tracking protein molecules through protein expression and purification. Furthermore, the characteristic absorbance signatures of the colored tags can be used to quantify protein concentrations directly, which allows purification to be linked to colorimetric detection. This technology, which we call Rainbow Tagging, facilitates expression and downstream processing of recombinant proteins, paving the way for the development of automated high-throughput protein expression systems.

ZEC, a zinc finger protein with novel binding specificity and transcription regulatory activity

A novel 114-kDa zinc finger protein, ZEC, has been found by cDNA cloning and characterized. ZEC was strongly expressed in the testis, liver and kidney, and also in embryonic stem cells. Epitope-tagged experiments indicated nuclear localization of ZEC. ZEC contained 18 C2H2 zinc fingers which were organized in two clusters. A ZEC binding DNA sequence, C/GA/TA/TGGTTGGTTGC, which we have designated the GT box, was identified by random oligonucleotide binding selection assay. The GT box did not contain binding sites for other previously characterized transcription factors and thus represented a potentially novel DNA target sequence. Electrophoretic mobility shift assay (EMSA) showed that both clusters of zinc fingers bound to the same DNA sequence. Site-directed mutagenesis revealed that the core sequence TTGGTT within the GT box was essential to ZEC binding, while DNA sequences outside of the core sequence enhanced this interaction. Furthermore, co-transfection assays demonstrated that ZEC could activate a reporter luciferase gene driven by this DNA sequence.

The proximal islet-specific glucose-6-phosphatase catalytic subunit-related protein autoantigen promoter is sufficient to initiate but not maintain transgene expression in mouse islets in vivo

We have previously reported the discovery of an islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) that is predominantly expressed in islet beta-cells. IGRP has recently been identified as a major autoantigen in a mouse model of type 1 diabetes. The analysis of IGRP-chloramphenicol acetyltransferase (CAT) fusion gene expression in transiently transfected islet-derived hamster insulinoma tumor and betaTC-3 cells revealed that the promoter region located between -306 and +3 confers high-level reporter gene expression. To determine whether this same promoter region is sufficient to confer islet beta-cell-specific gene expression in vivo, it was ligated to a beta-galactosidase reporter gene, and transgenic mice expressing the resulting fusion gene were generated. In two independent founder lines, this -306 to +3 promoter region was sufficient to drive beta-galactosidase expression in newborn mouse islets, predominantly in beta-cells, which was initiated during the expected time in development, around embryonic day 12.5. However, unlike the endogenous IGRP gene, beta-galactosidase expression was also detected in the cerebellum. Moreover, beta-galactosidase expression was almost completely absent in adult mouse islets, suggesting that cis-acting elements elsewhere in the IGRP gene are required for determining appropriate IGRP tissue-specific expression and for the maintenance of IGRP gene expression in adult mice.

Characterization of Proteins Binding to E-box/Ku86 Sites and Function of Ku86 in Transcriptional Regulation of the Human Xanthine Oxidoreductase Gene

We reported previously that E-box and TATA-like elements repress human xanthine oxidoreductase gene (hXOR) expression. In the present investigation, we determined the means by which the E-box site functions in this basal repression. DNA affinity purification demonstrated that at least five proteins are involved in the nuclear protein complex binding to the E-box and adjacent Ku86-binding sites. Amino acid sequence analysis demonstrated that three proteins, DNA-PK catalytic subunit, Ku86, and Ku70 are components of DNA-dependent protein kinase (DNA-PK). By electrophoretic mobility shift assays, gel-shift, and site-directed mutagenesis, we confirmed Ku86 binding to the Ku86 site. Studies indicated that the other two proteins of the complex are AREB6-like proteins binding to the E-box. Pull-down and immunoprecipitation analyses demonstrated the binding of Ku86 to AREB6-like proteins. The functional loss of Ku86 increases hXOR promoter activity and transcript expression. Based on the findings, we propose that DNA-PK/AREB6-like proteins play a central role in repression of basal hXOR activity. AREB6-like proteins specifically bind to the E-box, whereas Ku86 binds an adjacent site and recruits DNA-PK catalytic subunit and Ku70 proteins. A working model is presented to account for the role of DNA-PK and AREB6-like proteins in regulating hXOR activity.

Cell-specific phosphorylation of Zfhep transcription factor

Zinc finger homeodomain enhancer-binding protein (Zfhep/Zfhx1a) is a transcription factor essential for immune system development, skeletal patterning, and life. Regulation of the interleukin-2 gene in T cells has been suggested to depend on post-translational processing of Zfhep, however, no modifications of Zfhep are known. Here we demonstrate that Zfhep is present in both hyperphosphorylated and hypophosphorylated forms. Western blot analysis demonstrates two forms of Zfhep with different mobilities. Differences in phosphorylation are sufficient to explain the difference in mobilities. Zfhep is primarily phosphorylated on Ser and Thr residues since PP2A dephosphorylates the slower mobility band. Treatment of nuclear extract with O-GlcNAcase did not detect O-linked sugar. Importantly, post-translational processing is cell-specific. Doublets of Zfhep were detected in five cell lines, whereas 6 cell lines contain only, or predominantly, non-phosphorylated Zfhep, and Saos-2 cells contain predominantly the phosphorylated form. These data provide the first demonstration that Zfhep is post-translationally modified.

Distribution of the transcription factors Sox9, AP-2, and [delta]EF1 in adult murine articular and meniscal cartilage and growth plate

The control of extracellular matrix (ECM) production is important for the development, maintenance, and repair of cartilage tissues. Matrix molecule synthesis is generally regulated by the rate of gene transcription determined by DNA transcription factors. We have shown that transcription factors Sox9, AP-2, and [delta]EF1 are able to alter the rate of CD-RAP transcription in vitro: Sox9 upregulates, AP-2 exhibits biphasic effects, and [delta]EF1 represses expression of the CD-RAP gene. To correlate these in vitro activities in vivo, transcription factors were co-immunolocalized with ECM proteins in three different cartilage tissues in which the rates of biosynthesis are quite different: articular, meniscal, and growth plate. Immunoreactivities of type II collagen and CD-RAP were higher in growth plate than in either the articular or meniscal cartilages and correlated positively with Sox9 protein. Sox9 staining decreased with hypertrophy and was low in articular and meniscal cartilages. In contrast, AP-2 and [delta]EF1 were low in proliferating chondrocytes but high in lower growth plate, articular, and meniscal cartilages. This increase was also accompanied by intense nuclear staining. These immunohistochemical results are the first to localize both [delta]EF1 and AP-2 to adult articular, meniscal, and growth plate cartilages and provide in vivo correlation of previous molecular biological studies.

Dynamic regulation of Brachyury expression in the amphibian embryo by XSIP1

Xenopus Brachyury (Xbra) plays a key role in mesoderm formation during early development. One factor thought to be involved in the regulation of Xbra is XSIP1, a zinc finger/homeodomain-like DNA-binding protein that belongs to the deltaEF1 family of transcriptional repressors. We show here that Xbra and XSIP1 are co-expressed at the onset of gastrulation, but that expression subsequently refines such that Xbra is expressed in prospective mesoderm and XSIP1 in anterior neurectoderm. This refinement of the expression patterns of the two genes is due in part to the ability of XSIP1 to repress expression of Xbra. This repression is highly specific, in the sense that XSIP1 does not repress the expression of other regionally expressed genes in the early embryo, and that other members of the family to which XSIP1 belongs, such as deltaEF1 and its Xenopus homologue ZEB, cannot regulate Xbra expression. The function of XSIP1 was studied further by making an interfering construct comprising the open reading frame of XSIP1 fused to the VP16 transactivation domain. Experiments using this chimeric protein suggest that XSIP1 is required for normal gastrulation movements to occur and for the development of the anterior neural plate.

Developmental and functional evidence of a role for Zfhep in neural cell development

The rat Zfhep gene encodes a member of the Zfh family of transcription factors having a homeodomain-like sequence and multiple zinc fingers. We examined expression of Zfhep in the rat forebrain during embryonic and postnatal development. Zfhep mRNA was strongly expressed in the progenitor cells of the ventricular zone around the lateral ventricles on E14 and E16, but showed little expression in cells that had migrated to form the developing cortex. Dual labeling with PCNA demonstrated expression of Zfhep mRNA in proliferating cells. Expression of Zfhep in the ventricular zone decreases during late development as the population of progenitor cells decreases. This pattern is distinctly different from other members of the Zfh family. We also examined the expression of Zfhep protein during retinoic acid-induced neurogenesis of P19 embryonal carcinoma cells. Zfhep is highly expressed in P19 neuroblasts, and expression decreases by the time of morphological neurogenesis. Hence, both P19 cells and embryonic brain demonstrate a loss of Zfhep expression during the transition from proliferating precursor to differentiated neural cells. We investigated a possible link between Zfhep and proliferation by treating human glial cell lines with Zfhep antisense phosphorothioate oligodeoxynucleotides. Two Zfhep antisense oligonucleotides repressed proliferation of either U-138 or U-343 glioblastoma cells more than control oligonucleotides. Based on the expression patterns of Zfhep in vivo and in the P19 cell model of neurogenesis, we suggest that Zfhep may play a role in proliferation or differentiation of neural cells.

T3-activation of the rat growth hormone gene is inhibited by a zinc finger/homeodomain protein

Since the transcription factor Zfhep is expressed in somatotropes and binds the rat growth hormone (rGH) gene T3-response element (TRE), we investigated whether Zfhep regulates the response of this gene to T3. In cotransfection experiments, Zfhep did not regulate the native rGH promoter in the absence of T3. However, Zfhep repressed T3-mediated activation significantly in either GH(3) or JEG-3 cells. Up to 70% repression was mediated through the rGH TRE in a heterologous promoter (thymidine kinase), but was not observed with the idealized DR4 or chicken lysozyme F2 TREs. Zfhep apparently does not repress T3-mediated activation simply by competition for binding to DNA since the C-terminal DNA-binding domain of Zfhep (which is sufficient for DNA-binding) is not sufficient for repression and since cotransfection of excess thyroid hormone receptor (TR) did not prevent repression by Zfhep. These data indicate that the rGH TRE is a composite element that can integrate Zfhep and T3 regulation.

Kheper, a novel ZFH/deltaEF1 family member, regulates the development of the neuroectoderm of zebrafish (Danio rerio)

Kheper is a novel member of the ZFH (zinc-finger and homeodomain protein)/deltaEF1 family in zebrafish. kheper transcripts are first detected in the epiblast of the dorsal blastoderm margin at the early gastrula stage and kheper is expressed in nearly all the neuroectoderm at later stages. kheper expression was expanded in noggin RNA-injected embryos and also in swirl mutant embryos and was reduced in bmp4 RNA-injected embryos and chordino mutant embryos, suggesting that kheper acts downstream of the neural inducers Noggin and Chordino. Overexpression of Kheper elicited ectopic expansion of the neuroectoderm-specific genes fkd3, hoxa-1, and eng3, and the ectopic expression of hoxa-1 was not inhibited by BMP4 overexpression. Kheper interacted with the transcriptional corepressors CtBP1 and CtBP2. Overexpression of a Kheper mutant lacking the homeodomain or of a VP16-Kheper fusion protein disturbed the development of the neuroectoderm and head structures. These data underscore the role of Kheper in the development of the neuroectoderm and indicate that Kheper acts as a transcriptional repressor.

Suppression of polydactyly of the Gli3 mutant (extra toes) by deltaEF1 homozygous mutation

Digit patterning is established through multiple genetic interactions. Delta-crystallin enhancer/E2-box factor (deltaEF1) is a zinc finger and homeodomain containing repressor protein, and is expressed in the posterior half of the forelimb bud and in the entire hindlimb bud during the early stage of limb development. The 6EF1-deficient mutant mice display various skeletal abnormalities, among which inferior ossification and abnormal patterning of autopodial bones are similar to those observed in Hox and Gli gene mutants. Gli3 mutant mice, extra toes (Xt), exhibit pre-axial polydactyly losing the identity of digit I. It is demonstrated here that deltaEF1null(lacZ) homozygosity suppressed formation of the extra digit, uniquely of the hindlimb, in both Gli3XtJ heterozygous and homozygous mutants, but with no restoration of digit I identity. In Gli3XtJ mutants, the Hoxd13 expression domain was expanded more dramatically in homozygotes. In Gli3XtJ;deltaEF1null(lacZ) double homozygous mutants, Hoxd13 expression once expanded in Gli3XtJ homozygous mutant was reduced, more conspicuously in the hindlimbs, which may account for hindlimb-restricted suppression of formation of the extra digit. The data suggest the possibility that the extent of Hoxd13 expression along the distal margin of the limb bud is determinative in defining the digit number.

XSIP1, a Xenopus zinc finger/homeodomain encoding gene highly expressed during early neural development

We have isolated a Xenopus homologue of the zinc finger/homeodomain-containing transcriptional repressor Smad-interacting protein-1 (SIP1) from mouse. XSIP1 is activated at the early gastrula stage and transcription occurs throughout embryogenesis. At the beginning of gastrulation, XSIP1 is strongly expressed in prospective neurectoderm. At the neurula stage, XSIP1 is highly expressed within the neural plate but weakly in the dorsal midline. At later stages of development transcripts are detected primarily within the neural tube and neural crest. In the adult, XSIP1 expression is detected at variable levels in several organs.

SIP1, a novel zinc finger/homeodomain repressor, interacts with Smad proteins and binds to 5'-CACCT sequences in candidate target genes

Activation of transforming growth factor beta receptors causes the phosphorylation and nuclear translocation of Smad proteins, which then participate in the regulation of expression of target genes. We describe a novel Smad-interacting protein, SIP1, which was identified using the yeast two-hybrid system. Although SIP1 interacts with the MH2 domain of receptor-regulated Smads in yeast and in vitro, its interaction with full-length Smads in mammalian cells requires receptor-mediated Smad activation. SIP1 is a new member of the deltaEF1/Zfh-1 family of two-handed zinc finger/homeodomain proteins. Like deltaEF1, SIP1 binds to 5'-CACCT sequences in different promoters, including the Xenopus brachyury promoter. Overexpression of either full-length SIP1 or its C-terminal zinc finger cluster, which bind to the Xbra2 promoter in vitro, prevented expression of the endogenous Xbra gene in early Xenopus embryos. Therefore, SIP1, like deltaEF1, is likely to be a transcriptional repressor, which may be involved in the regulation of at least one immediate response gene for activin-dependent signal transduction pathways. The identification of this Smad-interacting protein opens new routes to investigate the mechanisms by which transforming growth factor beta members exert their effects on expression of target genes in responsive cells and in the vertebrate embryo.

A zinc finger homeodomain transcription factor binds specific thyroid hormone response elements

Thyroid hormone receptors can act through response elements (TREs) having a wide variation of sequence. We screened for transcription factors that bind the rat (r) glycoprotein hormone alpha-subunit TRE (alpha-sub), and isolated a cDNA, termed zinc finger homeodomain enhancer-binding protein (Zfhep), which encodes two separate zinc finger domains (ZD1 and ZD2), and a region similar to homeodomains. DNA-binding assays show that ZD1 or ZD2 can bind the alpha-subunit, rat growth hormone, or thyrotropin beta (TSHbeta) gene TREs, but do not bind DR4 or palindromic (pal) TREs. Methylation interference footprinting demonstrates that Zfhep binds the alpha-sub overlapping the TR-binding site. Similarly, the ZD1 protein footprints over TR-binding halfsites of the rat growth hormone (rGH) and TSHbeta TREs. Hence, Zfhep binding is dependent on sequences within and outside the AGGTCA TR-binding halfsite. Interactions of non-receptor transcription factors (such as Zfhep) with certain TREs are important to modify gene-specific regulation by thyroid hormones.

DeltaEF1, a zinc finger and homeodomain transcription factor, is required for skeleton patterning in multiple lineages

DeltaEF1 is a DNA binding protein containing a homeodomain and two zinc finger clusters, and is regarded as a vertebrate homologue of zfh-1 (zinc finger homeodomain-containing factor-1) in Drosophila. In the developing embryo, deltaEF1 is expressed in the notochord, somites, limb, neural crest derivatives and a few restricted sites of the brain and spinal cord. To elucidate the regulatory function of deltaEF1 in mouse embryogenesis, we generated deltaEF1 null mutant (deltaEF1null(lacZ)) mice. The deltaEF1null(lacZ) homozygotes developed to term, but never survived postnatally. In addition to severe T cell deficiency of the thymus, the deltaEF1null(lacZ) homozygotes exhibited skeletal defects of various lineages. (1) Craniofacial abnormalities of neural crest origin: cleft palate, hyperplasia of Meckel's cartilage, dysplasia of nasal septum and shortened mandible. (2) Limb defects: shortening and broadening of long bones, fusion of carpal/tarsal bone and fusion of joints. (3) Fusion of ribs. (4) Sternum defects: split and asymmetric ossification pattern of the sternebrae associated with irregular sternocostal junctions. (5) Hypoplasia of intervertebral discs. These results indicate that deltaEF1 has an essential role in regulating development of these skeletal structures. Since the skeletal defects were not observed in deltaEF1deltaC727 mice, deltaEF1 bears distinct regulatory activities which are dependent on different domains of the molecule.

Impairment of T cell development in deltaEF1 mutant mice

Using the method of gene targeting in mouse embryonic stem cells, regulatory function of deltaEF1, a zinc finger and homeodomain-containing transcription factor, was investigated in vivo by generating the deltaEF1 mutant mice. The mutated allele of deltaEF1 produced a truncated form of the deltaEF1 protein lacking a zinc finger cluster proximal to COOH terminus. The homozygous deltaEF1 mutant mice had poorly developed thymi with no distinction of cortex and medulla. Analysis of the mutant thymocyte showed reduction of the total cell number by two orders of magnitude accompanying the impaired thymocyte development. The early stage intrathymic c-kit+ T precursor cells were largely depleted. The following thymocyte development also seemed to be affected as assessed by the distorted composition of CD4- or CD8-expressing cells. The mutant thymocyte showed elevated alpha4 integrin expression, which might be related to the T cell defect in the mutant mice. In the peripheral lymph node tissue of the mutant mice, the CD4-CD8+ single positive cells were significantly reduced relative to CD4+CD8-single positive cells. In contrast to T cells, other hematopoietic lineages appeared to be normal. The data indicated that deltaEF1 is involved in regulation of T cell development at multiple stages.

Organization of the gene encoding transcriptional repressor deltaEF1 and cross-species conservation of its domains

DeltaEF1 (delta-crystallin/E2-box factor 1) is a widely distributed repressor of transcription which binds at the E2-box sequence, CACCTG. It carries seven zinc fingers (Zf) in two clusters and a homeodomain in the middle as potential DNA-binding domains. We cloned the genomic gene encoding chicken deltaEF1 and analyzed its organization. The gene consisted of nine exons, the N-proximal Zf were encoded by exons 5 through 7, and the C-proximal Zf by exons 8 and 9. Exon 7 also coded for the large middle portion of the protein including the homeodomain. Promoter analysis and RNase-protection assay indicated that the gene is driven by a G+C-rich promoter without a TATA box, and the transcription start points (tsp) cluster around 20 bp from the start codon located in exon 1. cDNA and genomic sequences of the mouse delta EF1 were cloned and compared with the chicken sequence. The deduced amino acid (aa) sequence was highly conserved between the chicken and mouse deltaEF1, no only in DNA-binding motifs but also in other blocks (78% overall aa identity). More recently reported DNA-binding proteins, AREB6 (human) ZEB (human) and BZP (hamster), were attributed to homologues of deltaEF1, among which only AREB6 represented full-length sequence. It was also indicated that rodent deltaEF1 lacked exon 3.

Alternative splicing gives rise to two isoforms of Zfhep, a zinc finger/homeodomain protein that binds T3-response elements

We have previously isolated a cDNA for a transcription factor referred to as Zfhep (zinc finger homeodomain enhancer-binding protein) containing two separate zinc finger domains, ZD1 and ZD2, each of which binds DNA, and a homeodomain. The rat Zfhep cDNA lacks a 5'-methionine codon, present in some homologs from other species. Hence, the aim of this work was to isolate the 5'-end of the rat Zfhep cDNA. Zfhep-2 cDNA was isolated, having a total length of 2.5 kbp, including more than 1.1 kbp of novel sequence followed by 1.4 kbp identical to the Zfhep-1 clone. The 1.1 kbp of novel sequence contains multiple stop codons in all reading frames, suggesting that it represents the 5'-untranslated (5'-UT) region of the rat Zfhep-2 mRNA. However, the Zfhep-2 clone does not contain the extreme 5'-exon(s) of the Zfhep-1 coding sequence, possibly due to alternative splicing of Zfhep RNA. To distinguish between a splice junction versus an intron-exon junction, the polymerase chain reaction (PCR) with rat genomic DNA and junction-flanking primers from the Zfhep-2 sequence was conducted. No bands were amplified from the genomic DNA by two different pairs of primers, indicating that the Zfhep-2-specific sequence is not intronic. Ribonuclease protection assays were performed to investigate the expression of multiple Zfhep mRNAs. Two protected bands were detected, and both were identified in total RNA or mRNA of rat ovary, hindbrain, forebrain, heart, kidney, small intestine, and GH4C1 cells. Zfhep-2 represents about 20% of the Zfhep RNA in each tissue. Hence, two mRNAs are expressed in these tissues, confirming the alternative splicing. To confirm independently the presence of both Zfhep-2 and Zfhep-1 mRNAs, reverse transcriptase (RT)-PCR was done using primers that span the Zfhep splice site. Specific bands representing both RNAs were obtained. The Zfhep-2 PCR product was subcloned and DNA sequence analysis confirmed the absence of ATG codons near the 5'-end of the open reading frame. The theoretical translation of the Zfhep-2 clone predicts a smaller protein than Zfhep-1. In vitro translation in reticulocyte lysates showed that Zfhep-2 is about 40 kD smaller than Zfhep-1. Hence, Zfhep-2 apparently lacks most of the first zinc finger domain (ZD1) of Zfhep-1. Because the two zinc finger domains bind different DNA sequences, Zfhep-2 is predicted to bind to only a subset of genes recognized by Zfhep-1.

Cloning of a cDNA encoding a mouse transcriptional repressor displaying striking sequence conservation across vertebrates

The nucleotide sequence encoding an approx. 120-kDa transcriptional repressor (MEB1) was determined from a cDNA which was cloned from a mouse brain library. An alignment of the deduced amino-acid sequences of the putative functional domains of MEB1 with those from the human, hamster and chicken homologues reveals a dramatic degree of conservation.

Checklist: vertebrate homeobox genes

Up to now around 170 different homeobox genes have been cloned from vertebrate genomes. A compilation of the various isolates from mouse, chick, frog, fish and man is presented in the form of a concise checklist, including the designations from the original publications. Putative homologs from different species are aligned, and key characteristics of embryonic or adult expression domains, as well as mutant phenotypes are briefly indicated.